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Population genomics and local adaptation: genome wide analysis of transposable elements and natural population evolutionary trajectories.

Applicant Roulin Anne
Number 154724
Funding scheme Ambizione
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Ecology
Start/End 01.03.2015 - 28.02.2018
Approved amount 599'728.00
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Keywords (4)

Brachypodium distachyon; local adaptation; population genomics; transposable elements

Lay Summary (French)

Lead
Comprendre comment les populations s'adaptent localement à leur environnement constitue une question majeure en biologie évolutive. Si nous avons de larges connaissances théoriques et expérimentales sur ce sujet, les bases génétiques du processus d'adaptation locale restent à être élucidées. Avec ce projet et en utilisant la plante modèle Brachypodium distachyon, nous proposons d'étudier comment les éléments transposables (séquences d'ADN mobile dans le génome) influencent la diversité génétique et potentiellement la capacité d'adaptation. Plus spécifiquement, nous voulons répondre à 3 questions: 1) les éléments transposables créent-ils de la diversité génétique en populations naturelles 2) Cette diversité est-elle associée à une modification de l'expression des gènes 3) Cette diversité est-elle corrélée aux variations de l'habitat, i.e. les éléments transposables sont-ils à l'origine d'adaptation locale?
Lay summary

Les caractéristiques des habitats naturels varient dans le temps et dans l'espace créant entre populations des variations de pression de sélection opérant sur les traits phénotypiques. Si la sélection n'est pas contre-balancée par d'autres forces telles que la migration et la dérive génétique, alors les populations peuvent s'adapter localement à leur habitat. Puisque l'adaptation locale représente une source majeure du maintien de la diversité génétique, comprendre comment ce processus évolutif se met en place représente une question majeure et le défi de la biologie moderne est maintenant d'en identifier les bases génétiques. Alors que la plupart des études sur ce sujet porte sur l'identification de mutations ponctuelles responsables de variations phénotypiques en lien avec les variations des habitats locaux, nous voulons ici évaluer si les éléments transposables (séquences d'ADN mobiles dans le génome et principales composantes des génomes Eucaryotes) peuvent aussi être liés au processus d'adaptation locale. De manière surprenante, cette question n'a pour le moment été étudiée que partiellement chez Drosophila melanogaster et notre projet vise donc à développer nos connaissances dans ce domaine. En utilisant des techniques  modernes de séquençage chez la plante modèle Brachypodium distachyon, nous voulons répondre à 3 questions:1) les éléments transposables créent-ils de la diversité génétique 2) Cette diversité est-elle associée à une modification de l'expression des gènes 3) Cette diversité est-elle corrélée aux variations de l'habitat ? Grâce à cette étude, nous aurons donc une meilleure compréhension de la variation génétique imputable aux éléments transposables et de leur impact sur l'écologie et l'évolution des populations naturelles.


Direct link to Lay Summary Last update: 11.12.2014

Responsible applicant and co-applicants

Employees

Publications

Publication
Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the mediterranean grass Brachypodium   distachyon.
Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC (2018), Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the mediterranean grass Brachypodium   distachyon., in Genome Biologa and Evolution, 10((1)), 304-318.
Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with phenotypic variation.
Gordon S.P et al. (2017), Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with phenotypic variation., in Nature communication, 8, 2184.
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Collaboration

Group / person Country
Types of collaboration
Pr. Koen Geuten- UK Leuven Belgium (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Genetic Diversity Center (GDC-Eth Zürich) Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Uni-Zürich-Institute of Plant Biology-Plant Development Genetics group Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Associated projects

Number Title Start Funding scheme
182785 Impact of transposable elements on plant population evolution: insight from the model grass species brachypodium distachyon 01.10.2019 Project funding (Div. I-III)

Abstract

Local adaptation constitutes the first step of biological diversification and speciation. Thus, elucidating the genetic mechanisms underlying this evolutionary process remains a major question in biology. Yet, even though they constitute the main component of Eukaryote genomes, the role of transposable elements (TEs) in local adaption has been poorly studied. TEs are mobile DNA sequences which have the capacity to replicate and/or move from one location to another in their host genome. They can therefore have drastic impacts such as destruction of genes or altering their expression when inserting near them. TEs can undergo bursts of activity (often induced by environmental factors), leading to large number of novel insertions and/or transposition events. Their copy number and the potential genetic novelty they create can thus vary drastically between closely related lineages. The aim of my project is to unravel how TE activity influences population evolution and subsequently local adaptation in the plant model organism Brachypodium distachyon. The grass B. distachyon constitutes an ideal model to perform comparative genomics at the population scale. Its genome is relatively small for a plant organisms, harbors approximately 40% of transposable elements and is fully sequenced and assembled. In addition, populations are widely distributed in Europe and therefore occur in contrasting habitats. Taking advantage of next-generation sequencing tools and of the high quality of the reference genome, the first goal of this project is to re-sequence the genomes of 60 natural accessions of B. distachyon. With this sequence data, I plan to perform a comprehensive analysis of TE variability within these accessions. Namely, I want to address the following questions i) what is the genetic diversity triggered by TEs among populations? ii) how often and what types of TEs are active in the different populations? iii) can specific insertions be associated with local adaptations? Based on the results of these analyses, a subset of natural accessions will be chosen for transcriptome sequencing using RNAseq. Here, the goal is to infer whether the identified TE variants alter expressions of nearby genes or give rise to novel chimeric co-transcirpts. By performing for the first time a genome wide analysis of TE at the population level, the results should allow conclusions on how many and what types of TE-related genes are involved in adaptation to local environments. In a distinct line of research, an experiment in artificial evolution is planned. Here, I propose to produce retrotransposon constructs where the native promoter of the TE is replaced by inducible and/or constitutive promoters. The constructs are expected to create of strong and sudden transposition burst of retrotransposon insertions. Viable offspring will be tested for fitness gains or losses over multiple generations. This experiment should allow to simulate the effects of transposon bursts on population fitness and dynamics. This would also complement the classical comparative analysis of TEs which are usually done at the inter-specific level.
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